diff options
Diffstat (limited to 'scripts/variant-calling-bowtie-bwa-mem.scm')
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 21 |
1 files changed, 8 insertions, 13 deletions
diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 88498f6..5ddc1f6 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -35,17 +35,14 @@ (list "samtools" "sort" "-")) (command "samtools_markdup" (list "samtools" "markdup" "-" "-") - #:other '((stdout . "dedup.bam")))) - (list (output "dedup_bam" - #:source "samtools_markdup/stdout"))) + #:other '((stdout . "dedup.bam"))))) (command "samtools_index" - (list "samtools" "index" - (input "dedup_bam")) + (list "samtools" "index" (input "samtools_stdout")) #:outputs (list (output "indexed_dedup_bam" - #:binding '((glob . "$(inputs.dedup_bam.basename)")) + #:binding '((glob . "$(inputs.samtools_stdout.basename)")) #:other '((secondary-files . #(".bai"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.dedup_bam)")))))) + (listing . #("$(inputs.samtools_stdout)")))))) (pipeline "freebayes" (list (command "freebayes" (list "freebayes" "--ploidy" "1" @@ -56,16 +53,14 @@ (list "bcftools" "view" "-i" "QUAL > 10" "-Oz") - #:other `((stdout . ,(string-append prefix "_output.vcf.gz"))))) - (list (output "vcf" - #:source "bcftools_view/stdout"))) + #:other `((stdout . ,(string-append prefix "_output.vcf.gz")))))) (command "tabix" - (list "tabix" (input "vcf")) + (list "tabix" (input "freebayes_stdout")) #:outputs (list (output "indexed_vcf" - #:binding '((glob . "$(inputs.vcf.basename)")) + #:binding '((glob . "$(inputs.freebayes_stdout.basename)")) #:other '((secondary-files . #(".tbi"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.vcf)"))))))) + (listing . #("$(inputs.freebayes_stdout)"))))))) (list (output (string-append prefix "_output") #:source "tabix/indexed_vcf")))) |